GapMind for catabolism of small carbon sources

 

Alignments for a candidate for scrK in Synechococcus elongatus PCC 7942

Align Fructokinase; D-fructose kinase; Manno(fructo)kinase; EC 2.7.1.4 (characterized)
to candidate Synpcc7942_2111 Synpcc7942_2111 xylose repressor

Query= SwissProt::P23917
         (302 letters)



>FitnessBrowser__SynE:Synpcc7942_2111
          Length = 302

 Score = 96.7 bits (239), Expect = 6e-25
 Identities = 84/260 (32%), Positives = 111/260 (42%), Gaps = 28/260 (10%)

Query: 3   IGIDLGGTKTEVIALGDAGEQLYRHRLPTPRDDYRQTIETIATLVDMAEQATGQRGT--V 60
           IG+DLGGT  ++      G+      +PTP       +   A LV+   Q   Q     +
Sbjct: 8   IGVDLGGTAMKLGRYTIEGQCQQELTVPTPTPSTPSNVR--AALVEAIRQLDPQAEALAI 65

Query: 61  GMGIPGSISPYTGVVKNA-NSTWLNGQPFDKDLSARLQREVRLANDANCLAVSEAVDGAA 119
           G+G PG       V + A N       P    L A LQR V LANDANC  + E   G  
Sbjct: 66  GIGTPGPADAAGRVARVAINLDGWTEVPLADWLEADLQRPVILANDANCAGLGEVWLGGG 125

Query: 120 AGAQTVFAVIIGTGCGAGVAFNGRAHIGGNGTAGEWGHNPLPWMDEDELRYREEVPCYCG 179
            G +    + +GTG G  +  NG   +G  GTA E G   L  +D           C  G
Sbjct: 126 RGYRDAILLTLGTGVGGAIVLNGELFVGRTGTAAELG---LITLDP------AGPHCNSG 176

Query: 180 KQGCIETFIS----GTGFAMDYRRLSGHALKGSEIIRLVEESDPVAELALRRYELRLAKS 235
            QG +E + S       F  D + L   A +G          DP A  A + Y   LA  
Sbjct: 177 NQGSLEQYASIGAVQRRFGCDPKDLGDRASQG----------DPEAIAAWQDYGRTLAAG 226

Query: 236 LAHVVNILDPDVIVLGGGMS 255
           LA +V +L P+VI+LGGG+S
Sbjct: 227 LASLVYVLTPEVIILGGGIS 246


Lambda     K      H
   0.318    0.137    0.418 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 298
Number of extensions: 19
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 302
Length of database: 302
Length adjustment: 27
Effective length of query: 275
Effective length of database: 275
Effective search space:    75625
Effective search space used:    75625
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory